Variant report

Variant	rs17664478
Chromosome Location	chr7:55992072-55992073
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:55985004..55987429-chr7:55990598..55992997,2	MCF-7	breast:
2	chr7:55979940..55982331-chr7:55990429..55992641,2	K562	blood:
3	chr7:55973351..55975048-chr7:55990434..55993161,2	K562	blood:

Variant related genes	Relation type
ENSG00000178665	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs17172508	0.93[CEU][hapmap]
rs3966180	0.92[CEU][hapmap]
rs4443615	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4495378	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4948095	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4948098	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4948107	0.91[CEU][hapmap]
rs4948108	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs5023487	1.00[ASW][hapmap]
rs66485869	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66741911	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6947109	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6964563	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73132850	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73132884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73132888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73134793	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73134796	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73138732	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73138736	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73138750	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73140745	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73140778	0.81[EUR][1000 genomes]
rs7784730	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7791221	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7808487	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7810142	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs872294	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv427782	chr7:55703073-56010314	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1019400	chr7:55709827-56094540	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
8	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
10	nsv888064	chr7:55831721-56104539	Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
12	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
13	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
14	nsv1034826	chr7:55962159-56092835	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv1033225	chr7:55962159-56094540	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	nsv607034	chr7:55974028-56002247	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv365792	chr7:55990238-55995589	Weak transcription Strong transcription ZNF genes & repeats Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17664478	CHCHD2	cis	Whole Blood	GTEx
rs17664478	ZNF713	cis	cerebellum	SCAN
rs17664478	CHCHD2	cis	parietal	SCAN
rs17664478	CHCHD2	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:55955400-56004200	Weak transcription	Gastric	stomach
2	chr7:55956200-56002200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr7:55956400-55995800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:55956400-55998800	Weak transcription	Colon Smooth Muscle	Colon
5	chr7:55962000-55992800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr7:55967600-55995800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr7:55968600-55995000	Weak transcription	HSMM	muscle
8	chr7:55969800-55998200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:55971600-55993400	Weak transcription	Primary B cells from cord blood	blood
10	chr7:55971800-55992800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:55974200-55994800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr7:55974400-55995600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr7:55974800-55993200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr7:55975000-56002000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr7:55975400-55995000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr7:55975600-55992800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr7:55975600-55992800	Weak transcription	Fetal Intestine Small	intestine
18	chr7:55975800-56006800	Weak transcription	Fetal Kidney	kidney
19	chr7:55976800-55994400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr7:55977200-55992400	Weak transcription	Small Intestine	intestine
21	chr7:55977200-55994400	Weak transcription	Hela-S3	cervix
22	chr7:55977800-55997600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr7:55978600-55995400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr7:55978800-55999400	Weak transcription	Placenta	Placenta
25	chr7:55979000-55994200	Weak transcription	NH-A	brain
26	chr7:55980000-55999000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr7:55980000-56001400	Weak transcription	Spleen	Spleen
28	chr7:55980400-56004000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr7:55980600-55999400	Weak transcription	Psoas Muscle	Psoas
30	chr7:55980600-56001200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr7:55980600-56004200	Weak transcription	Right Ventricle	heart
32	chr7:55980800-55995400	Weak transcription	A549	lung
33	chr7:55980800-55999400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr7:55981000-55993600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:55981400-55992600	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr7:55981600-55995600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr7:55982400-55995000	Weak transcription	Fetal Thymus	thymus
38	chr7:55982600-56006200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr7:55984000-55998200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr7:55984200-55992800	Weak transcription	Left Ventricle	heart
41	chr7:55984400-55993200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr7:55984800-55997000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr7:55985800-55999600	Weak transcription	Dnd41	blood
44	chr7:55986200-55993400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr7:55986200-55996000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr7:55986600-55992200	Weak transcription	Lung	lung
47	chr7:55986600-56006800	Weak transcription	Fetal Brain Male	brain
48	chr7:55988400-55996400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr7:55989600-55994800	Strong transcription	Fetal Stomach	stomach
50	chr7:55990200-55994800	Strong transcription	Fetal Muscle Leg	muscle

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